let the project finally begin..

hey guys. i been really busy lately, just moved back to Baltimore, MD in late Feb. but i got a job an shit an thas jus helpin me out wit bill but im bout to get a new job so i really get my project kickin. but anyway onto the topic, im still wantin to do the auto to 5spd swap, i have been researching and reading alot, basicly every day and night so im going to attempt everything myself and with a buddy of mine. but i went to the junkyard the other day and picked up parts 4 the 5speed swap. what im going to do is do a 5speed swap and motor swap at the same time so i do it right the 1st an spend less money as much as i possibly can. but any way i picked up the clutch master an slave cylinders, and the whole clutch pedal assembly for $40. good deal. got everything from an EG. now what im trying to figure out with the motor swap is the shift linkage, do i use the linkage from a donor car like mine or the one that comes with the swap? same thing with the axels?what i plan on dropping in is a b16. also need a little help with the whole obd..since my car is obd2 an the b16s on hmotorsonline.com are obd1, will i have to get a whole new wiring harness or just get a jumper harness? so if anyone can help me understand things a lil better ill appriciate it as i keep reading on..